added StructureOverpaintHelper.setFromExpression and alpha prop

src/mol-plugin/util/structure-overpaint-helper.ts

 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,10 +7,12 @@
 import { PluginStateObject } from '../../mol-plugin/state/objects';
 import { StateTransforms } from '../../mol-plugin/state/transforms';
 import { StateSelection, StateObjectCell, StateTransform, StateBuilder } from '../../mol-state';
-import { Structure, StructureElement } from '../../mol-model/structure';
+import { Structure, StructureElement, StructureSelection, QueryContext } from '../../mol-model/structure';
 import { PluginContext } from '../context';
 import { Color } from '../../mol-util/color';
 import { Overpaint } from '../../mol-theme/overpaint';
+import Expression from '../../mol-script/language/expression';
+import { compile } from '../../mol-script/runtime/query/compiler';
 
 type OverpaintEachReprCallback = (update: StateBuilder.Root, repr: StateObjectCell<PluginStateObject.Molecule.Structure.Representation3D, StateTransform<typeof StateTransforms.Representation.StructureRepresentation3D>>, overpaint?: StateObjectCell<any, StateTransform<typeof StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle>>) => void
 const OverpaintManagerTag = 'overpaint-controls'
@@ -29,7 +31,7 @@ export class StructureOverpaintHelper {
         await this.plugin.runTask(state.updateTree(update, { doNotUpdateCurrent: true }));
     }
 
-    async set(color: Color | -1, lociGetter: (structure: Structure) => StructureElement.Loci, types?: string[]) {
+    async set(color: Color | -1, lociGetter: (structure: Structure) => StructureElement.Loci, types?: string[], alpha = 1) {
         await this.eachRepr((update, repr, overpaintCell) => {
             if (types && !types.includes(repr.params!.values.type.name)) return
 
@@ -48,15 +50,23 @@ export class StructureOverpaintHelper {
             if (overpaintCell) {
                 const bundleLayers = [ ...overpaintCell.params!.values.layers, layer ]
                 const filtered = getFilteredBundle(bundleLayers, structure)
-                update.to(overpaintCell).update(Overpaint.toBundle(filtered, 1))
+                update.to(overpaintCell).update(Overpaint.toBundle(filtered, alpha))
             } else {
                 const filtered = getFilteredBundle([ layer ], structure)
                 update.to(repr.transform.ref)
-                    .apply(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, Overpaint.toBundle(filtered, 1), { tags: OverpaintManagerTag });
+                    .apply(StateTransforms.Representation.OverpaintStructureRepresentation3DFromBundle, Overpaint.toBundle(filtered, alpha), { tags: OverpaintManagerTag });
             }
         })
     }
 
+    async setFromExpression(color: Color | -1, expression: Expression, types?: string[], alpha = 1) {
+        return this.set(color, (structure) => {
+            const compiled = compile<StructureSelection>(expression)
+            const result = compiled(new QueryContext(structure))
+            return StructureSelection.toLociWithSourceUnits(result)
+        }, types, alpha)
+    }
+
     constructor(private plugin: PluginContext) {
 
     }